Have you tried manually selecting 3D mode from the video menu? It hardly ever switches automatically for me, even when it shows as 3D, but when I switch 3D mode off and on again from the video menu, it causes the screen to switch to the correct mode.

Late response from but does Kodi show your movie as 3D in the library? I've had some issues with files not named correctly and as a result Kodi did not play it as 3D correctly.This page on the kodi wiki helped me a lot: 3D - Official Kodi Wiki It seemed that adding HSBS, HOU or HTAB in addition to the 3D in the filename did the trick for me.